1  Setting up R and RStudio

Author

Affiliation

Daniela Palleschi

Humboldt-Universität zu Berlin

This document outlines the steps required to set up our reproducible workflow. Chapter 2 provides an overview of installing R, RStudio, and required packages. These steps are required. Chapter 3 describes how to install TinyTex, which is required to render LaTeX-style documents (i.e., PDFs) in R.

?sec-zotero provides tips on installing Zotero and related addins for integrations with R and RStudio. This is optional, and slightly more advanced.

2 R and RStudio

Download R here.

Download RStudio here.

You must first download R, then RStudio.

2.1 Packages

R packages available on the Comprehensive R Archive Network, commonly known as CRAN repository, can be easily installed using the command isntall.packages("packageName"). Some packages we will be needing are:

• here package
• tidyverse family of packages
  • will automatically include packages we need, like dplyr and ggplot2

To download multiple packages at once, use the ‘concatenate’ function in r (c()) inside install.packages():

install.packages(c("here", 
                   "tidyverse",
                   "pacman"))

2.2 Developer packages (optional)

Not all packages are available on CRAN. You will need to install them directly through the developer. Two packages that are commonly used to do this are remotes and devools. Let’s try installing remotes and then installing the rbbt, an addin for Zotero (discussed below).

if(!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")

remotes::install_github("paleolimbot/rbbt")

2.2.1 kableExtra for table formatting

remotes::install_github("haozhu233/kableExtra")

2.2.2 quartoExtra

For dark/light mode toggle: https://debruine.github.io/quarto_demo/quartoExtra.html

devtools::install_github("debruine/quartoExtra")

2.3 RStudio Global options (optional)

Here are my preferred global options (RStudio > Tools > Global options). I highly recommend following the settings for ‘workspace’ and ‘R Sessions’ to ensure reproducibility. The other settings you can play around with to find what you like.

• General > Basic
  • Workspace (for reproducibile workflow!!!)
    • uncheck ‘Restore .RData into workshapce at startup’
    • Save workspace to .RData on exit: Never
  • R Sessions
    • uncheck ‘Restore previously open source documents at startup’
• Code > Display
  • General
    • Show white space characters
    • Allow scroll past end of document
    • highlight selected line
• Appearance
  • Editor theme: Cobalt

3 tinyTex

To render PDF documents with LaTeX under the hood, we need to install tinytex. There are different ways to do this:

• run the following in the terminal: quarto install tinytex
• or in the console: tinytex::install_tinytex()

4 webR

In the Terminal:

quarto add coatless/quarto-webr

Then add WebR filter to slides in the YAML:

format: revealjs
filters:
  - webr

5 timesaveR

e.g., for the as_tribble() function

remotes::install_github('lukaswallrich/timesaveR')

6 glossary

https://debruine.github.io/glossary/

install.packages("glossary")